├── .gitignore ├── LICENSE ├── README.md ├── pystan2 ├── _extensions │ └── quarto-ext │ │ └── include-code-files │ │ ├── _extension.yml │ │ └── include-code-files.lua ├── _includes │ ├── apply_transform.qmd │ ├── check_all_expectand_diagnostics.qmd │ ├── check_all_hmc_diagnostics.qmd │ ├── check_ess_hat.qmd │ ├── check_inc_tau_hat.qmd │ ├── check_rhat.qmd │ ├── check_tail_xi_hats.qmd │ ├── check_variances.qmd │ ├── compile_model.qmd │ ├── compute_min_ess_hats.qmd │ ├── compute_rhos.qmd │ ├── compute_split_rhat.qmd │ ├── compute_split_rhats.qmd │ ├── compute_tail_xi_hats.qmd │ ├── compute_tau_hat.qmd │ ├── compute_xi_hat.qmd │ ├── display_ave_accept_proxy.qmd │ ├── display_stepsizes.qmd │ ├── ensemble_mcmc_est.qmd │ ├── ensemble_mcmc_quantile_est.qmd │ ├── eval_expectand_pushforward.qmd │ ├── eval_expectand_pushforwards.qmd │ ├── eval_uni_expectand_pushforward.qmd │ ├── extract_expectand_vals.qmd │ ├── extract_hmc_diagnostics.qmd │ ├── filter_expectands.qmd │ ├── implicit_subset_prob.qmd │ ├── mcmc_est.qmd │ ├── name_array.qmd │ ├── name_nested_list.qmd │ ├── plot_div_pairs.qmd │ ├── plot_empirical_correlogram.qmd │ ├── plot_expectand_pushforward.qmd │ ├── plot_inv_metric.qmd │ ├── plot_num_leapfrogs.qmd │ ├── plot_num_leapfrogs_by_chain.qmd │ ├── plot_pairs_by_chain.qmd │ ├── split_chain.qmd │ ├── summarize_expectand_diagnostics.qmd │ └── welford_summary.qmd ├── custom.scss ├── generate_includes ├── mcmc_analysis_tools_pystan2.py ├── misc │ └── save_fit.py ├── pystan2_demo.html ├── pystan2_demo.pdf ├── pystan2_demo.qmd ├── pystan2_demo.tex └── stan_programs │ ├── bernoulli_linear.stan │ └── simu_logistic_reg.stan ├── pystan3 ├── _extensions │ └── quarto-ext │ │ └── include-code-files │ │ ├── _extension.yml │ │ └── include-code-files.lua ├── _includes │ ├── apply_transform.qmd │ ├── check_all_expectand_diagnostics.qmd │ ├── check_all_hmc_diagnostics.qmd │ ├── check_ess_hat.qmd │ ├── check_inc_tau_hat.qmd │ ├── check_rhat.qmd │ ├── check_tail_xi_hats.qmd │ ├── check_variances.qmd │ ├── compute_min_ess_hats.qmd │ ├── compute_rhos.qmd │ ├── compute_split_rhat.qmd │ ├── compute_split_rhats.qmd │ ├── compute_tail_xi_hats.qmd │ ├── compute_tau_hat.qmd │ ├── compute_xi_hat.qmd │ ├── display_ave_accept_proxy.qmd │ ├── display_stepsizes.qmd │ ├── ensemble_mcmc_est.qmd │ ├── ensemble_mcmc_quantile_est.qmd │ ├── eval_expectand_pushforward.qmd │ ├── eval_expectand_pushforwards.qmd │ ├── eval_uni_expectand_pushforward.qmd │ ├── extract_expectand_vals.qmd │ ├── extract_hmc_diagnostics.qmd │ ├── filter_expectands.qmd │ ├── implicit_subset_prob.qmd │ ├── mcmc_est.qmd │ ├── name_array.qmd │ ├── name_nested_list.qmd │ ├── plot_div_pairs.qmd │ ├── plot_empirical_correlogram.qmd │ ├── plot_expectand_pushforward.qmd │ ├── plot_inv_metric.qmd │ ├── plot_num_leapfrogs.qmd │ ├── plot_num_leapfrogs_by_chain.qmd │ ├── plot_pairs_by_chain.qmd │ ├── split_chain.qmd │ ├── summarize_expectand_diagnostics.qmd │ └── welford_summary.qmd ├── generate_includes ├── mcmc_analysis_tools_pystan3.py ├── pystan3_demo.html ├── pystan3_demo.pdf ├── pystan3_demo.qmd ├── pystan3_demo.tex └── stan_programs │ ├── bernoulli_linear.stan │ └── simu_logistic_reg.stan └── rstan ├── _extensions └── quarto-ext │ └── include-code-files │ ├── _extension.yml │ └── include-code-files.lua ├── _includes ├── apply_transform.qmd ├── check_all_expectand_diagnostics.qmd ├── check_all_hmc_diagnostics.qmd ├── check_ess_hat.qmd ├── check_inc_tau_hat.qmd ├── check_rhat.qmd ├── check_tail_xi_hats.qmd ├── check_variances.qmd ├── compute_min_ess_hats.qmd ├── compute_rhos.qmd ├── compute_split_rhat.qmd ├── compute_split_rhats.qmd ├── compute_tail_xi_hats.qmd ├── compute_tau_hat.qmd ├── compute_xi_hat.qmd ├── display_ave_accept_proxy.qmd ├── display_stepsizes.qmd ├── elem_names.qmd ├── ensemble_mcmc_est.qmd ├── ensemble_mcmc_quantile_est.qmd ├── eval_expectand_pushforward.qmd ├── eval_expectand_pushforwards.qmd ├── eval_uni_expectand_pushforward.qmd ├── 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